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Cubeviz spectral extraction to ignore NaNs by masking them out #2737

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Mar 5, 2024
Merged

Cubeviz spectral extraction to ignore NaNs by masking them out #2737

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6692c9c
TST: Add a regression test
pllim Mar 1, 2024
730aea0
Fix the bug
pllim Mar 1, 2024
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2 changes: 2 additions & 0 deletions CHANGES.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -97,6 +97,8 @@ Bug Fixes
Cubeviz
^^^^^^^

- Spectral extraction now ignores NaNs. [#2737]

Imviz
^^^^^

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3 changes: 3 additions & 0 deletions jdaviz/configs/cubeviz/plugins/spectral_extraction/spectral_extraction.py
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Expand Up @@ -272,6 +272,9 @@ def collapse_to_spectrum(self, add_data=True, **kwargs):
else:
wcs = spectral_cube.coords.spectral

# Filter out NaNs (False = good)
mask = np.logical_or(mask, np.isnan(flux))

nddata_reshaped = NDDataArray(
flux, mask=mask, uncertainty=uncertainties, wcs=wcs, meta=nddata.meta
)
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13 changes: 13 additions & 0 deletions jdaviz/configs/cubeviz/plugins/spectral_extraction/tests/test_spectral_extraction.py
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Expand Up @@ -356,3 +356,16 @@ def test_cone_aperture_with_frequency_units(cubeviz_helper, spectral_cube_wcs):

with pytest.raises(ValueError, match="Spectral axis unit physical type is"):
extract_plg.collapse_to_spectrum()


def test_cube_extraction_with_nan(cubeviz_helper, image_cube_hdu_obj):
image_cube_hdu_obj[1].data[:, :2, :2] = np.nan
cubeviz_helper.load_data(image_cube_hdu_obj, data_label="with_nan")
extract_plg = cubeviz_helper.plugins['Spectral Extraction']
sp = extract_plg.collapse_to_spectrum() # Default settings (sum)
assert_allclose(sp.flux.value, 96) # (10 x 10) - 4

cubeviz_helper.load_regions(RectanglePixelRegion(PixCoord(1.5, 1.5), width=4, height=4))
extract_plg.aperture = 'Subset 1'
sp_subset = extract_plg.collapse_to_spectrum() # Default settings but on Subset
assert_allclose(sp_subset.flux.value, 12) # (4 x 4) - 4
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